I never run anything like it if not in safe mode, I don't think any app can remove stuff that is in use. But tbh i always thought of it as a clean up utility and it always removed crap left over from a normal uninstall.
But for shits and giggles i ran it on mine, in regular windows mode, and behold my usb ports also stopped functioning as well. We both have z77 boards so I am sure something is going on here with intel drivers